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Lin Z, He H, Xian Y, Cai J, Ge Q, Guo M, Zheng Q, Liu X, Mo C, Zhang X, Qi W, Zhang Y, Liang L, Yu X, Zhu YZ. Discovery of deoxyandrographolide and its novel effect on vascular senescence by targeting HDAC1. MedComm (Beijing) 2023; 4:e338. [PMID: 37600507 PMCID: PMC10435835 DOI: 10.1002/mco2.338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Aconitum carmichaelii (Fuzi) is a traditional Chinese medicine that has been widely used in the clinic to save the dying life for over several thousand years. However, the medicinal components of Fuzi in treating vascular senescence (VS) and its potential mechanism remain unclear. In this study, a network pharmacology method was used to explore the possible components and further validated by experiments to get a candidate compound, deoxyandrographolide (DA). DA restrains aging biomarkers, such as p16, p21, γH2A.X, and p53 in vitro and in vivo blood co-culture studies. Histone deacetylase 1 (HDAC1), mouse double minute2 (MDM2), cyclin-dependent kinase 4, and mechanistic target of rapamycin kinase (mTOR) are predicted to be the possible targets of DA based on virtual screening. Subsequent bio-layer interferometry results indicated that DA showed good affinity capability with HDAC1. DA enhances the protein expression of HDAC1 in the angiotensin II-induced senescence process by inhibiting its ubiquitination degradation. Loss of HDAC1 by CRISPR/Cas9 leads to the disappearance of DA's anti-aging property. The enhancement of HDAC1 represses H3K4me3 (a biomarker of chromosomal activity) and improves chromosome stability. RNA sequencing results also confirmed our hypothesis. Our evidence illuminated that DA may achieve as a novel compound in the treatment of VS by improving chromosome stability.
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Affiliation(s)
- Zhongxiao Lin
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and The Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Hao He
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Yu Xian
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Jianghong Cai
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Qinyang Ge
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Minghao Guo
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Quan Zheng
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Xiaoyan Liu
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Chengke Mo
- Guangzhou Twelfth People's HospitalGuangzhouChina
| | - Xin Zhang
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Wei Qi
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Lu Liang
- Department of PharmacologyShanghai Key Laboratory of Bioactive Small MoleculesSchool of PharmacyFudan UniversityShanghaiChina
| | - Xi‐Yong Yu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and The Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Yi Zhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine and School of PharmacyMacau University of Science and TechnologyMacauChina
- Department of PharmacologyShanghai Key Laboratory of Bioactive Small MoleculesSchool of PharmacyFudan UniversityShanghaiChina
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Joshi S, Natteshan NVS, Rastogi R, Sampathkumar A, Pandimurugan V, Sountharrajan S. A novel artificial intelligence approach to detect the breast cancer using KNNet technique with EPM gene profiling. Funct Integr Genomics 2023; 23:302. [PMID: 37721631 DOI: 10.1007/s10142-023-01227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/15/2023] [Accepted: 09/02/2023] [Indexed: 09/19/2023]
Abstract
Women's most frequent type of cancer is breast cancer, second only to lung cancer. This paper summarizes changes in genomics and epigenetics and incremental biological activities. A tumour develops through a series of phases involving a separate abnormal gene. Even though many diseases cause DNA mutations, most treatments are designed to relieve symptoms rather than change the DNA. Clustering short palindromic repeats (CRISPR) or Cas9 is the primary approach for discovering and confirming tumorigenic genomic targets. A Kohonen neural network with an expression programming model was developed for gene selection. The main problem in genetic selection is reducing the number of features chosen while maintaining accuracy. This purpose is accomplished systematically. In the end, the approach method performed better than the existing quantum squirrel-inspired algorithm and the recurrent neural network oppositional call search algorithm for genetic selection. The KNNet-EPM model used an expression programming approach to identify gene biomarkers for breast cancer. This method was achieved with RAE of 42%, sensitivity of 93%, f1 score of 88%, accuracy of 98%, kappa score of 83%, specificity of 92% and MAE of 30%.
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Affiliation(s)
- Shubham Joshi
- Department of Computer Science Engineering, Symbiosis Institute of Technology, Symbiosis International (Deemed) University, Pune, India
| | - N V S Natteshan
- School of Computing, Kalasalingam Academy of Research and Education, Krishnan Koil, TN, India
| | - Ravi Rastogi
- Department of CSE, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - A Sampathkumar
- Department of Applied Cybernetics, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
| | - V Pandimurugan
- School of Computing, Department of Networking and Communications, SRMIST, Kattankulathur Campus, Chennai, 603203, India
| | - S Sountharrajan
- Department of Computer Science and Engineering, Amrita School of Computing, Amrita Vishwa Vidyapeetham, Chennai, India
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Xiao X, Huang Y, Zhang J, Cao Y, Zhang M. Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing. Funct Integr Genomics 2023; 23:114. [PMID: 37000337 DOI: 10.1007/s10142-023-01012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 04/01/2023]
Abstract
Both Warrensburg (WS) and Marfan syndrome (MFS) can impair the vision. Here, we recruited a Chinese family consisting of two WS affected individuals (II:1 and III:3) and five MFS affected individuals( I:1, II:2, III:1, III:2, and III:5) as well as one suspected MFS individual (II:4). Using whole exome sequencing (WES) and subsequent PCR-Sanger sequencing, we identified one novel heterozygous variant NM_000438 (PAX3) c.208 T > C, (p.Cys70Arg) from individuals with WS and one previous reported variant NM_000138 (FBN1) c.2740 T > A, (p.Cys914Ser) from individuals with MFS and co-segregated with the diseases. Real-time PCR and Western blot assay showed that, compared to their wild-type, both mRNAs and proteins of PAX3 and FBN1 mutants reduced in HKE293T cells. Together, our study identified two disease-causing variants in a same Chinese family with WS and MFS, and confirmed their damaged effects on their genes' expression. Therefore, those findings expand the mutation spectrum of PAX3 and provide a new perspective for the potential therapy.
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Affiliation(s)
- Xiaoqiang Xiao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China.
| | - Yuqiang Huang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Jianqiang Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yingjie Cao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
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Liu Y, Niu Y, Ma X, Xiang Y, Wu D, Li W, Wang T, Niu D. Porcine endogenous retrovirus: classification, molecular structure, regulation, function, and potential risk in xenotransplantation. Funct Integr Genomics 2023; 23:60. [PMID: 36790562 DOI: 10.1007/s10142-023-00984-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
Xenotransplantation with porcine organs has been recognized as a promising solution to alleviate the shortage of organs for human transplantation. Porcine endogenous retrovirus (PERV), whose proviral DNAs are integrated in the genome of all pig breeds, is a main microbiological risk for xenotransplantation. Over the last decades, some advances on PERVs' studies have been achieved. Here, we reviewed the current progress of PERVs including the classification, molecular structure, regulation, function in immune system, and potential risk in xenotransplantation. We also discussed the problem of insufficient study on PERVs as well as the questions need to be answered in the future work.
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Affiliation(s)
- Yu Liu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yifan Niu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Xiang Ma
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.,College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.,Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China
| | - Yun Xiang
- Jinhua Academy of Agricultural Sciences, Jinhua, Zhejiang, 321000, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, Zhejiang, 321000, China
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Tao Wang
- Nanjing Kgene Genetic Engineering Co., Ltd, Nanjing, Jiangsu, 211300, China.
| | - Dong Niu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.
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Conner MM, Schaner Tooley CE. Three's a crowd - why did three N-terminal methyltransferases evolve for one job? J Cell Sci 2023; 136:jcs260424. [PMID: 36647772 PMCID: PMC10022744 DOI: 10.1242/jcs.260424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
N-terminal methylation of the α-amine group (Nα-methylation) is a post-translational modification (PTM) that was discovered over 40 years ago. Although it is not the most abundant of the Nα-PTMs, there are more than 300 predicted substrates of the three known mammalian Nα-methyltransferases, METTL11A and METTL11B (also known as NTMT1 and NTMT2, respectively) and METTL13. Of these ∼300 targets, the bulk are acted upon by METTL11A. Only one substrate is known to be Nα-methylated by METTL13, and METTL11B has no proven in vivo targets or predicted targets that are not also methylated by METTL11A. Given that METTL11A could clearly handle the entire substrate burden of Nα-methylation, it is unclear why three distinct Nα-methyltransferases have evolved. However, recent evidence suggests that many methyltransferases perform important biological functions outside of their catalytic activity, and the Nα-methyltransferases might be part of this emerging group. Here, we describe the distinct expression, localization and physiological roles of each Nα-methyltransferase, and compare these characteristics to other methyltransferases with non-catalytic functions, as well as to methyltransferases with both catalytic and non-catalytic functions, to give a better understanding of the global roles of these proteins. Based on these comparisons, we hypothesize that these three enzymes do not just have one common function but are actually performing three unique jobs in the cell.
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Affiliation(s)
- Meghan M. Conner
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Christine E. Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
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Chen H, Xie C, Chen Q, Zhuang S. HDAC11, an emerging therapeutic target for metabolic disorders. Front Endocrinol (Lausanne) 2022; 13:989305. [PMID: 36339432 PMCID: PMC9631211 DOI: 10.3389/fendo.2022.989305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Histone deacetylase 11 (HDAC11) is the only member of the class IV HDAC, and the latest member identified. It is highly expressed in brain, heart, kidney and some other organs, and located in mitochondria, cytoplasm and nuclei, depending on the tissue and cell types. Although studies in HDAC11 total knockout mice suggest its dispensable features for tissue development and life, it participates in diverse pathophysiological processes, such as DNA replication, tumor growth, immune regulation, oxidant stress injury and neurological function of cocaine. Recent studies have shown that HDAC11 is also critically involved in the pathogenesis of some metabolic diseases, including obesity, diabetes and complications of diabetes. In this review, we summarize the recent progress on the role and mechanism of HDAC11 in the regulation of metabolic disorders, with the focus on its regulation on adipogenesis, lipid metabolism, metabolic inflammation, glucose tolerance, immune responses and energy consumption. We also discuss the property and selectivity of HDAC11 inhibitors and their applications in a variety of in vitro and in vivo models of metabolic disorders. Given that pharmacological and genetic inhibition of HDAC11 exerts a beneficial effect on various metabolic disorders, HDAC11 may be a potential therapeutic target to treat chronic metabolic diseases.
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Affiliation(s)
- Huizhen Chen
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunguang Xie
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiu Chen
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, United States
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